This Codon optimisation tool was developed by team Sydney Australia for iGEM 2015. 
For more information see: http://2015.igem.org/Team:Sydney_Australia/TransOpt

Run the tool using TransOpt.m
Different sequences can be optimised, just save them as a text file in the working directory, and point to them in the TransOpt file.
Different organisms can be utilised as initial / heterologous expression hosts - download their properties and put them in a csv file as done here for Mycobacterium, Pseudomonas, and E-Coli.

The data fro Mycobacterium is from here:
http://gtrnadb.ucsc.edu/Myco_smeg_MC2_155/

Pseudomonas:
http://gtrnadb.ucsc.edu/Pseu_puti_KT2440/

E coli:
http://gtrnadb.ucsc.edu/Esch_coli_K12/